Arrggghhhh..... sorry, later I list-upgrades again:
# pear upgrade Net_DNS-beta
downloading Net_DNS-1.0.0rc3.tgz ...
Starting to download Net_DNS-1.0.0rc3.tgz (26,775 bytes)
.........done: 26,775 bytes
upgrade ok: channel://pear.php.net/Net_DNS-1.0.0rc3
[root@ancilla pear-core]# pear -d preferred_state=alpha list-upgrades
pear.php.net Available Upgrades (alpha, beta, stable):
======================================================
Channel Package Local Remote Size
pear.php.net Auth 1.2.3 (stable) 1.3.0r3 (beta) 34kB
pear.php.net Config 1.10.4 (stable) 1.10.5 (stable) 25kB
pear.php.net Net_DNS 1.0.0rc3 (beta) 1.0.0b3 (beta) 26kB
# cat /tmp/pear/cache/049a7fd34e096a5eb5ad9ca410339efarest.cachefile
a:14:{s:7:"attribs";a:2:{s:5:"xmlns";s:36:"http://pear.php.net/dtd/rest.release";s:18:"xsi:schemaLocation";s:81:"http://pear.php.net/dtd/rest.releasehttp://pear.php.net/dtd/rest.release.xsd";}s:1:"p";a:2:{s:7:"attribs";a:1:{s:10:"xlink:href";s:15:"/rest/p/net_dns";}s:8:"_content";s:7:"Net_DNS";}s:1:"c";s:12:"pear.php.net";s:1:"v";s:7:"1.0.0b3";s:2:"st";s:4:"beta";s:1:"l";s:8:"LGPL 2.1";s:1:"m";s:8:"ekilfoil";s:1:"s";s:54:"Resolver library used to communicate with a DNS server";s:1:"d";s:341:"A resolver library used to communicate with a name server to perform DNS queries, zone transfers, dynamic DNS updates, etc. Creates an object hierarchy from a DNS server's response, which allows you to view all of the information given by the DNS server. It bypasses the system's resolver library and communicates directly with the server.";s:2:"da";s:19:"2005-04-09 11:19:24";s:1:"n";s:49:"Fixed all pending bugs
Ensured php5 compatibility";s:1:"f";s:5:"25818";s:1:"g";s:39:"http://pear.php.net/get/Net_DNS-1.0.0b3";s:1:"x";a:1:{s:7:"attribs";a:1:{s:10:"xlink:href";s:19:"package.1.0.0b3.xml";}}}
$ cat /tmp/pear/cache/134bec37164ef1fce55587aca2a9583drest.cachefile
a:14:{s:7:"attribs";a:2:{s:5:"xmlns";s:36:"http://pear.php.net/dtd/rest.release";s:18:"xsi:schemaLocation";s:81:"http://pear.php.net/dtd/rest.releasehttp://pear.php.net/dtd/rest.release.xsd";}s:1:"p";a:2:{s:7:"attribs";a:1:{s:10:"xlink:href";s:15:"/rest/p/net_dns";}s:8:"_content";s:7:"Net_DNS";}s:1:"c";s:12:"pear.php.net";s:1:"v";s:8:"1.0.0rc3";s:2:"st";s:4:"beta";s:1:"l";s:16:"PHP License 3.01";s:1:"m";s:4:"bate";s:1:"s";s:55:"Resolver library used to communicate with a DNS server.";s:1:"d";s:335:"A resolver library used to communicate with a name server to perform DNS queries, zone transfers, dynamic DNS updates, etc.
Creates an object hierarchy from a DNS server response, which allows you to view all of the information given by the DNS server. It bypasses the system resolver library and communicates directly with the server.";s:2:"da";s:19:"2005-12-01 04:40:04";s:1:"n";s:112:"* Added new parameter for class constructor
array with configuration values for the
Net_DNS_Resolver() class";s:1:"f";s:5:"26775";s:1:"g";s:40:"http://pear.php.net/get/Net_DNS-1.0.0rc3";s:1:"x";a:1:{s:7:"attribs";a:1:{s:10:"xlink:href";s:20:"package.1.0.0rc3.xml";}}}
Extract of rest.categorypackageinfo:
------------------------------------
i:11;a:3:{s:1:"p";a:7:{s:1:"n";s:7:"Net_DNS";s:1:"c";s:12:"pear.php.net";s:2:"ca";a:2:{s:7:"attribs";a:1:{s:10:"xlink:href";s:18:"/rest/c/Networking";}s:8:"_content";s:10:"Networking";}s:1:"l";s:16:"PHP License 3.01";s:1:"s";s:55:"Resolver library used to communicate with a DNS server.";s:1:"d";s:335:"A resolver library used to communicate with a name server to perform DNS queries, zone transfers, dynamic DNS updates, etc.
Creates an object hierarchy from a DNS server response, which allows you to view all of the information given by the DNS server. It bypasses the system resolver library and communicates directly with the server.";s:1:"r";a:1:{s:7:"attribs";a:1:{s:10:"xlink:href";s:15:"/rest/r/net_dns";}}}s:1:"a";a:1:{s:1:"r";a:9:{i:0;a:2:{s:1:"v";s:8:"1.0.0rc3";s:1:"s";s:4:"beta";}i:1;a:2:{s:1:"v";s:8:"1.0.0rc2";s:1:"s";s:4:"beta";}i:2;a:2:{s:1:"v";s:8:"1.0.0rc1";s:1:"s";s:4:"beta";}i:3;a:2:{s:1:"v";s:7:"1.0.0b3";s:1:"s";s:4:"beta";}i:4;a:2:{s:1:"v";s:6:"1.00b2";s:1:"s";s:4:"beta";}i:5;a:2:{s:1:"v";s:6:"1.00b1";s:1:"s";s:4:"beta";}i:6;a:2:{s:1:"v";s:4:"0.03";s:1:"s";s:6:"stable";}i:7;a:2:{s:1:"v";s:4:"0.02";s:1:"s";s:5:"alpha";}i:8;a:2:{s:1:"v";s:4:"0.01";s:1:"s";s:5:"devel";}}}s:4:"deps";a:9:{i:0;a:2:{s:1:"v";s:8:"1.0.0rc1";s:1:"d";s:154:"a:2:{i:1;a:3:{s:4:"type";s:3:"php";s:3:"rel";s:2:"ge";s:7:"version";s:3:"4.2";}i:2;a:3:{s:4:"type";s:3:"ext";s:3:"rel";s:3:"has";s:4:"name";s:5:"mhash";}}";}i:1;a:2:{s:1:"v";s:7:"1.0.0b3";s:1:"d";s:154:"a:2:{i:1;a:3:{s:4:"type";s:3:"php";s:3:"rel";s:2:"ge";s:7:"version";s:3:"4.2";}i:2;a:3:{s:4:"type";s:3:"ext";s:3:"rel";s:3:"has";s:4:"name";s:5:"mhash";}}";}i:2;a:2:{s:1:"v";s:6:"1.00b2";s:1:"d";s:4:"b:0;";}i:3;a:2:{s:1:"v";s:6:"1.00b1";s:1:"d";s:4:"b:0;";}i:4;a:2:{s:1:"v";s:4:"0.03";s:1:"d";s:4:"b:0;";}i:5;a:2:{s:1:"v";s:4:"0.02";s:1:"d";s:4:"b:0;";}i:6;a:2:{s:1:"v";s:4:"0.01";s:1:"d";s:4:"b:0;";}i:7;a:2:{s:1:"v";s:8:"1.0.0rc2";s:1:"d";s:202:"a:2:{i:1;a:4:{s:4:"type";s:3:"php";s:3:"rel";s:2:"ge";s:7:"version";s:3:"4.2";s:8:"optional";s:2:"no";}i:2;a:4:{s:4:"type";s:3:"ext";s:3:"rel";s:3:"has";s:8:"optional";s:2:"no";s:4:"name";s:5:"mhash";}}";}i:8;a:2:{s:1:"v";s:8:"1.0.0rc3";s:1:"d";s:202:"a:2:{i:1;a:4:{s:4:"type";s:3:"php";s:3:"rel";s:2:"ge";s:7:"version";s:3:"4.2";s:8:"optional";s:2:"no";}i:2;a:4:{s:4:"type";s:3:"ext";s:3:"rel";s:3:"has";s:8:"optional";s:2:"no";s:4:"name";s:5:"mhash";}}";}}}

OK, the issue has been discovered.
version_compare() thinks that 1.0.0rc3 != 1.0.0RC3
This is in fact clearly documented at http://www.php.net/version_compare
We need to amend the coding standards ASAP to reflect this change, because 1.0.0rc3 is NOT the same as 1.0.0RC3, and is considered to be < 1.0.0b3!!

This bug has been fixed in CVS.
If this was a documentation problem, the fix will appear on pear.php.net by the end of next Sunday (CET).
If this was a problem with the pear.php.net website, the change should be live shortly.
Otherwise, the fix will appear in the package's next release.
Thank you for the report and for helping us make PEAR better.